Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various
intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes …

Escherichia coli is considered to be the best-known microorganism given the large number
of published studies detailing its genes, its genome and the biochemical functions of its …

Background Species-level genetic characterization of complex bacterial communities has
important clinical applications in both diagnosis and treatment. Amplicon sequencing of the …

Escherichia coli is the most researched microbial organism in the world. Its varied impact on
human health, consisting of commensalism, gastrointestinal disease, or extraintestinal …

Figure 1 iML1515 genome-scale reconstruction.(a) The iML1515 model contains 1,515
open reading frames that encode enzymes that catalyze 2,719 reactions involving 1,192 …

Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are
not in a parent–offspring relationship. HGT is a widely recognized mechanism for adaptation …

Since the first two complete bacterial genome sequences were published in 1995, the
science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is …

Most current approaches for analyzing metagenomic data rely on comparisons to reference
genomes, but the microbial diversity of many environments extends far beyond what is …

Fast and accurate identification and typing of pathogens are essential for effective
surveillance and outbreak detection. The current routine procedure is based on a variety of …

The existence of large amounts of within-species genome content variability is puzzling.
Population genetics tells us that fitness effects of new variants—either deleterious, neutral or …